HuManN v4 output are different

Microbial community profiling HUMAnN
1

Hello to everyone!

I downloaded HuManN from the GitHub web site (GitHub - biobakery/humann: HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).) so I should have the version number 3 but when I check (humann --version) I have the v4.0. Do you know why?

When I run my data the output are a bit different, I do not have the pathway coverage file but a reactions file.

Also when I look at my gene family file, I just have I species and a t_ that I do not understand what is, where I can find the family and the gender?

Thank you!

2

I had the same issue before. I think you should install through conda instead.

3

Indeed, it sounds like you pulled the HUMAnN 4 alpha source code, but we have not published the full databases for HUMAnN 4 yet, so you’d only be seeing demo-style output.

4

Ok thank you! Also because when I run it I have the errore that the version vOct22 does not have the head line but I would like to use the version vJun23 (202403) for Metaphlan. How I can do? I have to wait for the new version?

5

Sorry I’m not following your question. You want to use the newest MetaPhlAn with the newest MetaPhlAn database? If so, that is discussed here:

6

No, sorry if I do not explain myself correctly. I want to use humann 3.9 with the vJun23_202403 database version of Metaphlan but I don’t know if it is possible.